scholarly journals Expressed sequence tag-PCR markers for identification of alien barley chromosome 2H in wheat

2012 ◽  
Vol 11 (3) ◽  
pp. 3452-3463
Author(s):  
M.J. Wang ◽  
H.D. Zou ◽  
Z.S. Lin ◽  
Y. Wu ◽  
X. Chen ◽  
...  
Keyword(s):  
Expressed Sequence Tag ◽  
Barley Chromosome ◽  
Pcr Markers ◽  
Expressed Sequence

Relationships among blueberry species within the section Cyanococcus of the Vaccinium genus based on EST-PCR markers

2021 ◽  
Author(s):  
Lisa Jeannine Rowland ◽  
Elizabeth L. Ogden ◽  
James R. Ballington
Keyword(s):  
Polymerase Chain Reaction ◽  
Expressed Sequence Tag ◽  
Clustering Methods ◽  
Polyploid Species ◽  
Pcr Markers ◽  
Chain Reaction ◽  
Ploidy Levels ◽  
Commercial Species ◽  
Polymerase Chain ◽  
Expressed Sequence

Commercial blueberry species of North America belong to the Vaccinium genus, section Cyanococcus. Phylogenetic relationships of 50 accessions of different ploidy levels within Cyanococcus were investigated using 249 expressed sequence tag-polymerase chain reaction markers and standard clustering methods. Of the commercial species, tetraploid V. corymbosum grouped most closely with the diploids, V. fuscatum and V. caesariense, followed by the diploid V. elliottii. Tetraploid V. angustifolium grouped with the diploids, V. boreale and V. myrtilloides. Hexaploid V. virgatum grouped most closely with the diploid V. tenellum, thus shedding light on the origins of these polyploid species.

scholarly journals Utility of Blueberry-derived EST-PCR Primers in Related Ericaceae Species

HortScience ◽  
2003 ◽  
Vol 38 (7) ◽  
pp. 1428-1432 ◽  
Author(s):  
Lisa J. Rowland ◽  
Anik L. Dhanaraj ◽  
James J. Polashock ◽  
Rajeev Arora
Keyword(s):  
Genetic Diversity ◽  
Dna Fingerprinting ◽  
Expressed Sequence Tag ◽  
Cdna Clones ◽  
Pcr Markers ◽  
Complex Species ◽  
The Family ◽  
Successful Amplification ◽  
Expressed Sequence ◽  
Pcr Primer

Expressed sequence tag-polymerase chain reaction (EST-PCR) markers for DNA fingerprinting and mapping in blueberry (Vaccinium sp.) had previously been developed from expressed sequence tags (ESTs) produced from a cDNA library, derived from RNA from floral buds of cold acclimated plants. Because EST-PCR markers are derived from gene coding regions, they are more likely to be conserved across populations and species than markers derived from random regions of DNA, such as randomly amplified polymorphic DNA (RAPD) or amplified fragment length polymorphism (AFLP) markers. In this study, we tested whether many of the EST-PCR primer pairs developed for blueberry are capable of amplifying DNA fragments in other members of the family Ericaceae. In addition, we cloned and sequenced a selection of 13 EST-PCR fragments to determine if they showed homology to the original blueberry cDNA clones from which the EST-PCR primer pairs were derived. Closely related cranberry genotypes (two wild selections of V. oxycoccus L. and two cultivars of V. macrocarpon Aiton, `Early Black' and `Stevens') and more distantly related rhododendron genotypes (one wild selection each of Rhododendron arboreum Marsh, R. maximum L., and R. ponticum L. and three complex species hybrids, `Sonata', `Grumpy Yellow', and `Roseum elegans') were used. Of 26 primer pairs tested in cranberry, 23 (89%) resulted in successful amplification and eight of those (35%) amplified polymorphic fragments among the cranberry genotypes. Of 39 primer pairs tested in rhododendron, 29 (74%) resulted in successful amplification and 21 of those (72%) amplified polymorphic fragments among the rhododendron genotypes. Approximately 50% of the 13 sequenced EST-PCR fragments were found to be homologous to the original blueberry cDNA clones. These markers should be useful for DNA fingerprinting, mapping, and assessing genetic diversity within cranberry and rhododendron species. The markers which are shown to be homologous to the blueberry cDNA clones by DNA sequencing should also be useful for comparative mapping and genetic diversity studies between some genera of the family Ericaceae.

Survey of a cDNA library from the turkey (Meleagris gallopavo)

Genome ◽  
2005 ◽  
Vol 48 (1) ◽  
pp. 12-17 ◽  
Author(s):  
L D Chaves ◽  
J A Rowe ◽  
K M Reed
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Expressed Sequence Tags ◽  
Expressed Sequence Tag ◽  
Meleagris Gallopavo ◽  
Whole Genome Sequence ◽  
Snp Discovery ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Important Species ◽  
Expressed Sequence

Genome characterization and analysis is an imperative step in identifying and selectively breeding for improved traits of agriculturally important species. Expressed sequence tags (ESTs) represent a transcribed portion of the genome and are an effective way to identify genes within a species. Downstream applications of EST projects include DNA microarray construction and interspecies comparisons. In this study, 694 ESTs were sequenced and analyzed from a library derived from a 24-day-old turkey embryo. The 437 unique sequences identified were divided into 76 assembled contigs and 361 singletons. The majority of significant comparative matches occurred between the turkey sequences and sequences reported from the chicken. Whole genome sequence from the chicken was used to identify potential exon–intron boundaries for selected turkey clones and intron-amplifying primers were developed for sequence analysis and single nucleotide polymorphism (SNP) discovery. Identified SNPs were genotyped for linkage analysis on two turkey reference populations. This study significantly increases the number of EST sequences available for the turkey.Key words: turkey, cDNA, expressed sequence tag, single nucleotide polymorphism.

Screening and analysis of differentially expressed genes from an alien addition line of wheat Thinopyrum intermedium induced by barley yellow dwarf virus infection

Genome ◽  
2004 ◽  
Vol 47 (6) ◽  
pp. 1114-1121 ◽  
Author(s):  
Shu-Mei Jiang ◽  
Long Zhang ◽  
Jun Hu ◽  
Rui Shi ◽  
Guang-He Zhou ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Expressed Sequence Tag ◽  
Barley Yellow Dwarf Virus ◽  
Differentially Expressed ◽  
Addition Line ◽  
Alien Chromosome ◽  
Thinopyrum Intermedium ◽  
Barley Yellow Dwarf ◽  
Yellow Dwarf Virus ◽  
Expressed Sequence

The alien addition line TAI-27 contains a pair of chromosomes of Thinopyrum intermedium that carry resistance against barley yellow dwarf virus (BYDV). A subtractive library was constructed using the leaves of TAI-27, which were infected by Schizaphis graminum carrying the GAV strain of BYDV, and the control at the three-leaf stage. Nine differentially expressed genes were identified from 100 randomly picked clones and sequenced. Two of the nine clones were highly homologous with known genes. Of the remaining seven cDNA clones, five clones matched with known expressed sequence tag (EST) sequences from wheat and (or) barley whereas the other two clones were unknown. Five of the nine differentially expressed sequences (WTJ9, WTJ11, WTJ15, WTJ19, and WTJ32) were highly homologous (identities >94%) with ESTs from wheat or barley challenged with pathogens. These five sequences and another one (WTJ18) were also highly homologous (identities >86%) with abiotic stress induced ESTs in wheat or barley. Reverse Northern hybridization showed that seven of the nine differentially expressed cDNA sequences hybridized with cDNA of T. intermedium infected by BYDV. Three of these also hybridized with cDNA of line 3B-2 (a parent of TAI-27) infected by BYDV. The alien chromosome in TAI-27 was microdissected. The second round linker adaptor mediated PCR products of the alien chromosomal DNA were labeled with digoxygenin and used as the probe to hybridize with the nine differentially expressed genes. The analysis showed that seven differentially expressed genes were homologous with the alien chromosome of TAI-27. These seven differentially expressed sequences could be used as ESTs of the alien chromosome of TAI-27. This research laid the foundation for screening and cloning of new specific functional genes conferring resistance to BYDV and probably other pathogens.Key words: suppression subtractive hybridization (SSH), expressed sequence tag (EST), linker adaptor mediated polymerase chain reaction (LA-PCR), chromosome microdissection.

Characterization of expressed sequence tag-derived simple sequence repeat markers for 17 Linum species

Botany ◽  
2010 ◽  
Vol 88 (5) ◽  
pp. 537-543 ◽  
Author(s):  
Yong-Bi Fu ◽  
Gregory W. Peterson
Keyword(s):  
Simple Sequence Repeat ◽  
Expressed Sequence Tag ◽  
Sequence Repeat ◽  
Simple Sequence Repeat Markers ◽  
Linum Usitatissimum L ◽  
Evolutionary Studies ◽  
Expressed Sequence ◽  
Simple Sequence ◽  
Cultivated Flax

One major challenge in genetic and evolutionary studies of wild flax species is the lack of informative molecular markers. A set of 100 informative expressed sequence tag-derived simple sequence repeat (EST-SSR) primer pairs developed in cultivated flax ( Linum usitatissimum L.) were characterized on 35 Linum accessions representing 17 Linum species for their transferability to other Linum species. Ninety-nine primer pairs displayed scorable polymorphisms across 35 Linum samples and generated 627 bands likely from 121 loci. About 50% of the detected bands occurred only in three or fewer samples. A total of 393 bands, likely from 116 loci, were detected by 97 primer pairs in Linum bienne Mill. samples, but only up to 60 bands, likely from up to 39 loci, were revealed by 6 to 37 primer pairs in the samples of the other 15 Linum species. The L. bienne samples displayed 23.7% more EST-SSR variation than the L. usitatissimum samples. These characterized EST-SSR markers should be useful for future genetic diversity and evolutionary studies of Linum species, particularly for the progenitor of cultivated flax.

scholarly journals Development of an Expressed Sequence Tag (EST) Resource for Wheat (Triticum aestivumL.)

Genetics ◽  
2004 ◽  
Vol 168 (2) ◽  
pp. 585-593 ◽  
Author(s):  
G. R. Lazo ◽  
S. Chao ◽  
D. D. Hummel ◽  
H. Edwards ◽  
C. C. Crossman ◽  
...  
Keyword(s):  
Expressed Sequence Tag ◽  
Expressed Sequence

scholarly journals Integration of Expressed Sequence Tag Data Flanking Predicted RNA Secondary Structures Facilitates Novel Non-Coding RNA Discovery

PLoS ONE ◽  
2011 ◽  
Vol 6 (6) ◽  
pp. e20561 ◽  
Author(s):  
Paul M. Krzyzanowski ◽  
Feodor D. Price ◽  
Enrique M. Muro ◽  
Michael A. Rudnicki ◽  
Miguel A. Andrade-Navarro
Keyword(s):  
Expressed Sequence Tag ◽  
Secondary Structures ◽  
Rna Secondary Structures ◽  
Non Coding Rna ◽  
Expressed Sequence

Gene expression profile of rabbit cartilage by expressed sequence tag analysis

Gene ◽  
2008 ◽  
Vol 424 (1-2) ◽  
pp. 147-152 ◽  
Author(s):  
Hyuck Joon Kwon ◽  
Hidetoshi Akimoto ◽  
Yoshihiro Ohmiya ◽  
Kenichi Honma ◽  
Kazunori Yasuda
Keyword(s):  
Gene Expression ◽  
Gene Expression Profile ◽  
Expression Profile ◽  
Expressed Sequence Tag ◽  
Rabbit Cartilage ◽  
Expressed Sequence Tag Analysis ◽  
Expressed Sequence

scholarly journals Analysis of Expressed Sequence Tag Data and Gene Expression Profiles Involved in Conidial Germination of Fusarium oxysporum

2006 ◽  
Vol 72 (2) ◽  
pp. 1667-1671 ◽  
Author(s):  
Ye Deng ◽  
Haitao Dong ◽  
Qingchao Jin ◽  
Cheng'en Dai ◽  
Yongqi Fang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Protein Synthesis ◽  
Fusarium Oxysporum ◽  
Cdna Library ◽  
Expressed Sequence Tag ◽  
Expression Profiles ◽  
Cdna Array ◽  
Gene Expression Profiles ◽  
Conidial Germination ◽  
Expressed Sequence

ABSTRACT We obtained 3,372 tentative unique transcripts (TUTs) from a cDNA library of Fusarium oxysporum. A cDNA array with 3,158 TUTs was produced to analyze gene expression profiles in conidial germination. It seems that ras and other signaling genes, e.g., ccg, cooperatively initiate conidial germination in Fusarium by increasing protein synthesis.

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